title: Integrated search and alignment of protein structures.
abstract: BACKGROUND
  Identification and comparison of similar three-dimensional (3D) protein structures has become an even greater challenge in the face of the rapidly growing structure databases. Here, we introduce Vorometric, a new method that provides efficient search and alignment of a query protein against a database of protein structures. Voronoi contacts of the protein residues are enriched with the secondary structure information and a metric substitution matrix is developed to allow efficient indexing. The contact hits obtained from a distance-based indexing method are extended to obtain high-scoring segment pairs, which are then used to generate structural alignments.
  
  
  RESULTS
  Vorometric is the first to address both search and alignment problems in the protein structure databases. The experimental results show that Vorometric is simultaneously effective in retrieving similar protein structures, producing high-quality structure alignments, and identifying cross-fold similarities. Vorometric outperforms current structure retrieval methods in search accuracy, while requiring com-parable running times. Furthermore, the structural superpositions produced are shown to have better quality and coverage, when compared with those of the popular structure alignment tools.
  
  
  BACKGROUND
  Vorometric is available as a web service at http://bio.cse.ohio-state.edu/Vorometric
authors.affiliation: Department of Computer Engineering, Middle East Technical University, Ankara, Turkey. sacan@cse.ohio-state.edu
authors.forename: Ahmet
authors.initials: A
authors.lastname: Sacan
authors.forename: I Hakki
authors.initials: IH
authors.lastname: Toroslu
authors.forename: Hakan
authors.initials: H
authors.lastname: Ferhatosmanoglu
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D008958:Models, Molecular; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry; D020539:Sequence Analysis, Protein; D040681:Structural Homology, Protein
chemical_list: D011506:Proteins